I'm not sure what section to post this in, so i'll do it here. I use the FOMM to put my mods in the correct (or at least what I hope is correct) load order. I'm not sure how to use it to avoid having to copy and paste the ArchiveInvalidation additions. Also, i'm confused about the bsa function it contains. Anyone want to give me a quick walkthrough or show me a link where this is explained?

You can use either the Toggle Invalidation button in FOMM to deal with your invalidation needs or download http://www.fallout3nexus.com/downloads/file.php?id=944, install it and (normally) forget about it.

The http://www.gamesas.com/index.php?/forum/45-mods/ section has information on everything you need.